--- a/computeMatrix.xml	Fri Mar 31 18:30:53 2017 -0400
+++ b/computeMatrix.xml	Sun May 14 19:20:26 2017 -0400
@@ -7,14 +7,7 @@
     <expand macro="requirements" />
     <command>
 <![CDATA[
-        #import re
-        #import tempfile
-        #set bw_files=[]
-        #for $counter, $bigwig, in enumerate($scoreFileName):
-            #set identifier = re.sub('[^\s\w\-]', '_', str($bigwig.element_identifier))
-            ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
-            #silent $bw_files.append('%s_%s.bw' % ($identifier, $counter))
-        #end for
+        @multiple_input_bigwigs@
 
         #set bed_files=[]
         #for $counter, $rf, in enumerate($regionsFiles):
@@ -28,7 +21,7 @@
             $mode.mode_select
             --regionsFileName '#echo "' '".join($bed_files)#'
 
-            --scoreFileName '#echo "' '".join($bw_files)#'
+            --scoreFileName '#echo "' '".join($files)#'
 
             --outFileName '$outFileName'
 
@@ -79,6 +72,9 @@
                 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                     --scale $advancedOpt.scale
                 #end if
+                #if $advancedOpt.samplesLabel is not None and str($advancedOpt.samplesLabel) != '':
+                    --samplesLabel $advancedOpt.samplesLabel
+                #end if
 
                 @ADVANCED_OPTS_GTF@
 
@@ -94,10 +90,7 @@
                 help="File, in BED format, containing the regions to plot."/>
         </repeat>
 
-        <param name="scoreFileName" format="bigwig" type="data"
-            label="Score file" multiple="True"
-            help="You can generate a bigWig file from a BAM file using the
-            bamCoverage tool. (--scoreFileName)"/>
+        <expand macro="multiple_input_bigwigs" MIN="1" LABEL="Score file" TITLE="Score files"/>
 
         <conditional name="mode" >
             <param name="mode_select" type="select"
@@ -214,6 +207,15 @@
                     bias the average values. (--maxThreshold)"/>
                 <param name="scale" type="float" optional="True" label="Scaling factor"
                     help="If set, all values are multiplied by this number. (--scale)"/>
+                <param argument="--samplesLabel" type="text" size="30"
+                    label="Labels for the samples (each bigwig)"
+                    help="The default is to use the history item label. The sample labels should be separated by
+                    spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
+                    <sanitizer>
+                        <valid initial="string.printable">
+                        </valid>
+                    </sanitizer>
+                </param>
 
                 <expand macro="gtf_options" />
 
@@ -229,7 +231,7 @@
     <tests>
         <test>
             <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
-            <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
+            <param name="bigwigfiles" value="bamCoverage_result4.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="reference-point" />
             <param name="binSize" value="10" />
@@ -241,7 +243,7 @@
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="reference-point" />
             <param name="binSize" value="10" />
@@ -251,7 +253,7 @@
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="scale-regions" />
             <param name="endLabel" value="END" />